Whole Genome Sequencing of 100 Cassava Genomes

Cassava (Manihot esculenta) is a major staple crop in Africa. It is daily food source for 500 million people across the world. As compared to other major crops, cassava did not go through the modern breeding process, therefore, large amounts of genetic load (deleterious mutations) still exist in the cassava genome. Significant inbreeding depression was reported in cassava - 63% lower root yield was observed in first generation selfed plants. Identifying the genetic load can accelerate cassava breeding. In this project, we will whole-genome sequence 100 diverse cassava genomes at 30X to characterize the genetic load. We will perform 250 bps pair end sequencing on these genomes. The single molecule sequencing (eg. Nanopore or PacBio technologies) will also be used to contig reads. The SNPs will be identified using pipelines and approaches based on those developed for the maize genome resequencing and maize HapMap V2. Structural variations will also be evaluated. These variants will be useful for both this project, the NextGen Cassava project and the entire cassava research and breeding community. For the next step, we will annotate these variants and build models to predict genetic load in cassava. The predictions will help breeders purge deleterious mutations from cassava genome.